What is one example of indirect evidence that scientists use to study an atom?

Pretty much everything we know about atoms is indirect evidence. One can't really see atoms. We do see enough of their effects that we can, with confidence, describe the nature of atoms. Here at Jefferson Lab we have quite a few instruments to measure the properties and behavior of atoms. We use a few simple tricks to measure atoms. The most common method is to shoot the atoms through an easy-to-ionize gas or liquid. Argon is the most common that we use. As the atoms or even pieces of atoms fly through the gas electrons are stripped off of them and are left behind. We drift those loose electrons to a collection device, a wire or panel, and measure the charge. It is a little more complex than that, but it works well enough that we get consistent results. It's like putting together a puzzle that's missing some pieces. If you get enough pieces in the right place you can tell what the picture is even though it still has holes.